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Merged
keitaroyam merged 13 commits into from
Nov 18, 2024
Merged

Update metal containing entries #58

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27f7b1e
metal containing monomers updated using acedrg + metalcoord
keitaroyam Sep 7, 2024
2b80a27
Merge branch 'master' into update-metals
keitaroyam Sep 18, 2024
da80a8f
added previously not-updated cases
keitaroyam Sep 30, 2024
da4d2ee
added previously not-updated cases
keitaroyam Oct 1, 2024
237d3a1
updated CUA FS1 HGN P3C
keitaroyam Oct 2, 2024
f6cdbeb
metal-bond-only cases
keitaroyam Oct 4, 2024
8a9e3b1
sort out model_Cartn_x
keitaroyam Oct 4, 2024
3831bc1
VV2 fixed
keitaroyam Oct 4, 2024
abb2d86
HEM/HEC and links updated
keitaroyam Oct 6, 2024
1668839
FES/SF4/SF3-CYS links updated
keitaroyam Oct 6, 2024
f435a8c
Merge branch 'master' into update-metals
keitaroyam Oct 9, 2024
84332cf
updated metal entries using the latest metalCoord and acedrg
keitaroyam Nov 14, 2024
23ad918
fixed errors
keitaroyam Nov 14, 2024
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425 changes: 425 additions & 0 deletions 0/067.cif
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948 changes: 948 additions & 0 deletions 0/07D.cif
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366 changes: 366 additions & 0 deletions 0/08T.cif
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Original file line number Diff line number Diff line change
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data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
08T 08T . NON-POLYMER 42 30 .

data_comp_08T
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
08T BE BE BE BE 4.00 15.982 -44.636 44.163
08T PA PA P P 0 20.275 -45.545 41.305
08T PB PB P P 0 18.478 -45.070 43.585
08T "C5'" C5' C CH2 0 20.267 -43.692 39.438
08T "O5'" O5' O O2 0 21.004 -44.369 40.500
08T "C4'" C4' C CH1 0 21.192 -42.761 38.684
08T "O4'" O4' O O2 0 21.731 -41.795 39.609
08T "C3'" C3' C CH1 0 22.404 -43.418 38.003
08T "O3'" O3' O OH1 0 22.097 -43.617 36.626
08T "C2'" C2' C CH1 0 23.570 -42.440 38.232
08T "O2'" O2' O OH1 0 23.825 -41.632 37.099
08T "C1'" C1' C CH1 0 23.125 -41.578 39.422
08T N1 N1 N NRD6 0 27.564 -41.163 42.005
08T O1A O1A O OP -1 21.255 -46.144 42.245
08T O1B O1B O O 0 17.873 -46.452 43.434
08T F1 F1 F F -1 16.103 -45.574 45.392
08T C2 C2 C CR16 0 27.207 -40.811 40.765
08T O2A O2A O O 0 19.569 -46.476 40.387
08T O2B O2B O OP -1 19.574 -45.026 44.631
08T F2 F2 F F -1 15.440 -45.436 42.950
08T N3 N3 N NRD6 0 26.034 -40.951 40.157
08T O3A O3A O O2 0 19.196 -44.739 42.171
08T O3B O3B O OP -1 17.433 -43.990 43.791
08T F3 F3 F F -1 14.991 -43.492 44.497
08T C4 C4 C CR56 0 25.134 -41.537 40.966
08T C5 C5 C CR56 0 25.357 -41.956 42.265
08T C6 C6 C CR6 0 26.642 -41.755 42.803
08T N6 N6 N NH2 0 26.989 -42.107 44.041
08T N7 N7 N NRD5 0 24.209 -42.517 42.802
08T C8 C8 C CR15 0 23.331 -42.427 41.833
08T N9 N9 N NR5 0 23.823 -41.850 40.687
08T H1 H1 H H 0 19.887 -44.359 38.811
08T H2 H2 H H 0 19.521 -43.170 39.829
08T H3 H3 H H 0 20.656 -42.284 38.001
08T H4 H4 H H 0 22.625 -44.292 38.416
08T H5 H5 H H 0 22.691 -44.079 36.251
08T H6 H6 H H 0 24.385 -42.947 38.480
08T H7 H7 H H 0 24.563 -41.233 37.178
08T H8 H8 H H 0 23.257 -40.599 39.183
08T H10 H10 H H 0 27.886 -40.403 40.248
08T H12 H12 H H 0 27.807 -41.956 44.333
08T H13 H13 H H 0 26.400 -42.492 44.571
08T H14 H14 H H 0 22.446 -42.731 41.916

loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
08T PA P(OC)(OP)(O)2
08T PB P(OP)(O)3
08T "C5'" C(C[5]C[5]O[5]H)(OP)(H)2
08T "O5'" O(CC[5]HH)(PO3)
08T "C4'" C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>}
08T "O4'" O[5](C[5]N[5a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>}
08T "C3'" C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>}
08T "O3'" O(C[5]C[5]2H)(H)
08T "C2'" C[5](C[5]N[5a]O[5]H)(C[5]C[5]HO)(OH)(H){1|C<4>,1|H<1>,2|C<3>}
08T "O2'" O(C[5]C[5]2H)(H)
08T "C1'" C[5](N[5a]C[5a,6a]C[5a])(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|O<2>,2|N<2>,3|H<1>}
08T N1 N[6a](C[6a]C[5a,6a]N)(C[6a]N[6a]H){1|C<3>,1|N<2>}
08T O1A O(PO3)
08T O1B O(PO3)
08T F1 F
08T C2 C[6a](N[6a]C[5a,6a])(N[6a]C[6a])(H){1|C<3>,2|N<3>}
08T O2A O(PO3)
08T O2B O(PO3)
08T F2 F
08T N3 N[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]N[6a]H){1|C<4>,1|N<2>,2|C<3>}
08T O3A O(PO3)2
08T O3B O(PO3)
08T F3 F
08T C4 C[5a,6a](C[5a,6a]C[6a]N[5a])(N[5a]C[5a]C[5])(N[6a]C[6a]){1|C<4>,1|N<2>,1|N<3>,1|O<2>,3|H<1>}
08T C5 C[5a,6a](C[5a,6a]N[5a]N[6a])(C[6a]N[6a]N)(N[5a]C[5a]){1|C<3>,1|C<4>,1|H<1>}
08T C6 C[6a](C[5a,6a]C[5a,6a]N[5a])(N[6a]C[6a])(NHH){1|C<3>,1|H<1>,1|N<2>,1|N<3>}
08T N6 N(C[6a]C[5a,6a]N[6a])(H)2
08T N7 N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H){1|C<4>,1|N<3>,2|N<2>}
08T C8 C[5a](N[5a]C[5a,6a]C[5])(N[5a]C[5a,6a])(H){1|C<3>,1|C<4>,1|H<1>,1|N<2>,1|O<2>}
08T N9 N[5a](C[5a,6a]C[5a,6a]N[6a])(C[5]C[5]O[5]H)(C[5a]N[5a]H){1|H<1>,1|O<2>,2|C<3>,2|C<4>}
08T H1 H(CC[5]HO)
08T H2 H(CC[5]HO)
08T H3 H(C[5]C[5]O[5]C)
08T H4 H(C[5]C[5]2O)
08T H5 H(OC[5])
08T H6 H(C[5]C[5]2O)
08T H7 H(OC[5])
08T H8 H(C[5]N[5a]C[5]O[5])
08T H10 H(C[6a]N[6a]2)
08T H12 H(NC[6a]H)
08T H13 H(NC[6a]H)
08T H14 H(C[5a]N[5a]2)

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.value_dist_nucleus
_chem_comp_bond.value_dist_nucleus_esd
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
08T F1 BE SINGLE n 1.55 0.03 1.55 0.03
08T BE F3 SINGLE n 1.55 0.03 1.55 0.03
08T O3B BE SINGLE n 1.63 0.03 1.63 0.03
08T BE F2 SINGLE n 1.55 0.03 1.55 0.03
08T "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100
08T "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100
08T "C4'" "C3'" SINGLE n 1.532 0.0100 1.532 0.0100
08T "C3'" "C2'" SINGLE n 1.532 0.0103 1.532 0.0103
08T "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
08T "C4'" "O4'" SINGLE n 1.444 0.0100 1.444 0.0100
08T "C2'" "C1'" SINGLE n 1.528 0.0100 1.528 0.0100
08T "C5'" "O5'" SINGLE n 1.445 0.0200 1.445 0.0200
08T "O4'" "C1'" SINGLE n 1.423 0.0100 1.423 0.0100
08T "C1'" N9 SINGLE n 1.462 0.0102 1.462 0.0102
08T C2 N3 SINGLE y 1.329 0.0100 1.329 0.0100
08T N3 C4 DOUBLE y 1.344 0.0100 1.344 0.0100
08T PA O2A DOUBLE n 1.485 0.0100 1.485 0.0100
08T N1 C2 DOUBLE y 1.338 0.0100 1.338 0.0100
08T PA "O5'" SINGLE n 1.598 0.0100 1.598 0.0100
08T C4 N9 SINGLE y 1.374 0.0101 1.374 0.0101
08T C4 C5 SINGLE y 1.382 0.0100 1.382 0.0100
08T C8 N9 SINGLE y 1.371 0.0100 1.371 0.0100
08T PA O1A SINGLE n 1.485 0.0100 1.485 0.0100
08T PA O3A SINGLE n 1.601 0.0120 1.601 0.0120
08T N1 C6 SINGLE y 1.355 0.0106 1.355 0.0106
08T C5 C6 DOUBLE y 1.407 0.0100 1.407 0.0100
08T C5 N7 SINGLE y 1.388 0.0100 1.388 0.0100
08T PB O3A SINGLE n 1.620 0.0143 1.620 0.0143
08T N7 C8 DOUBLE y 1.311 0.0100 1.311 0.0100
08T C6 N6 SINGLE n 1.332 0.0107 1.332 0.0107
08T PB O1B DOUBLE n 1.516 0.0200 1.516 0.0200
08T PB O3B SINGLE n 1.516 0.0200 1.516 0.0200
08T PB O2B SINGLE n 1.516 0.0200 1.516 0.0200
08T "C5'" H1 SINGLE n 1.092 0.0100 0.991 0.0200
08T "C5'" H2 SINGLE n 1.092 0.0100 0.991 0.0200
08T "C4'" H3 SINGLE n 1.092 0.0100 0.990 0.0200
08T "C3'" H4 SINGLE n 1.092 0.0100 0.991 0.0200
08T "O3'" H5 SINGLE n 0.972 0.0180 0.839 0.0200
08T "C2'" H6 SINGLE n 1.092 0.0100 0.991 0.0200
08T "O2'" H7 SINGLE n 0.972 0.0180 0.839 0.0200
08T "C1'" H8 SINGLE n 1.092 0.0100 1.016 0.0200
08T C2 H10 SINGLE n 1.085 0.0150 0.946 0.0200
08T N6 H12 SINGLE n 1.013 0.0120 0.880 0.0200
08T N6 H13 SINGLE n 1.013 0.0120 0.880 0.0200
08T C8 H14 SINGLE n 1.085 0.0150 0.942 0.0168

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
08T BE O3B PB 109.47 5.0
08T O2A PA "O5'" 109.340 2.31
08T O2A PA O1A 118.805 3.00
08T O2A PA O3A 109.053 3.00
08T "O5'" PA O1A 109.340 2.31
08T "O5'" PA O3A 100.137 3.00
08T O1A PA O3A 109.053 3.00
08T O3A PB O1B 106.004 3.00
08T O3A PB O3B 106.004 3.00
08T O3A PB O2B 106.004 3.00
08T O1B PB O3B 112.609 3.00
08T O1B PB O2B 112.609 3.00
08T O3B PB O2B 112.609 3.00
08T "C4'" "C5'" "O5'" 109.454 1.61
08T "C4'" "C5'" H1 109.589 1.50
08T "C4'" "C5'" H2 109.589 1.50
08T "O5'" "C5'" H1 109.882 1.50
08T "O5'" "C5'" H2 109.882 1.50
08T H1 "C5'" H2 108.471 1.50
08T "C5'" "O5'" PA 116.362 1.50
08T "C3'" "C4'" "C5'" 115.288 1.50
08T "C3'" "C4'" "O4'" 105.318 1.50
08T "C3'" "C4'" H3 109.322 2.54
08T "C5'" "C4'" "O4'" 109.154 1.50
08T "C5'" "C4'" H3 108.351 1.59
08T "O4'" "C4'" H3 109.120 1.50
08T "C4'" "O4'" "C1'" 109.502 2.85
08T "O3'" "C3'" "C4'" 110.713 3.00
08T "O3'" "C3'" "C2'" 111.671 3.00
08T "O3'" "C3'" H4 110.541 2.08
08T "C4'" "C3'" "C2'" 102.593 1.50
08T "C4'" "C3'" H4 110.577 3.00
08T "C2'" "C3'" H4 110.454 1.85
08T "C3'" "O3'" H5 109.389 3.00
08T "O2'" "C2'" "C3'" 112.677 3.00
08T "O2'" "C2'" "C1'" 110.814 3.00
08T "O2'" "C2'" H6 110.904 1.50
08T "C3'" "C2'" "C1'" 101.406 1.50
08T "C3'" "C2'" H6 110.788 1.91
08T "C1'" "C2'" H6 110.342 1.91
08T "C2'" "O2'" H7 109.217 3.00
08T "C2'" "C1'" "O4'" 106.114 1.65
08T "C2'" "C1'" N9 113.380 2.77
08T "C2'" "C1'" H8 109.222 1.50
08T "O4'" "C1'" N9 108.577 1.50
08T "O4'" "C1'" H8 109.833 2.53
08T N9 "C1'" H8 109.411 1.50
08T C2 N1 C6 118.603 1.50
08T N3 C2 N1 129.210 1.50
08T N3 C2 H10 115.427 1.50
08T N1 C2 H10 115.363 1.50
08T C2 N3 C4 111.101 1.50
08T PA O3A PB 132.613 3.00
08T N3 C4 N9 127.848 1.50
08T N3 C4 C5 126.355 1.50
08T N9 C4 C5 105.797 1.50
08T C4 C5 C6 117.356 1.50
08T C4 C5 N7 110.646 1.50
08T C6 C5 N7 131.998 1.50
08T N1 C6 C5 117.375 1.50
08T N1 C6 N6 118.852 1.50
08T C5 C6 N6 123.773 1.50
08T C6 N6 H12 119.818 3.00
08T C6 N6 H13 119.818 3.00
08T H12 N6 H13 120.363 3.00
08T C5 N7 C8 103.906 1.50
08T N9 C8 N7 113.692 1.50
08T N9 C8 H14 122.949 1.50
08T N7 C8 H14 123.359 1.50
08T "C1'" N9 C4 126.969 2.94
08T "C1'" N9 C8 127.072 3.00
08T C4 N9 C8 105.958 1.50
08T F1 BE F2 109.47 5.0
08T F1 BE O3B 109.47 5.0
08T F1 BE F3 109.47 5.0
08T F2 BE O3B 109.47 5.0
08T F2 BE F3 109.47 5.0
08T O3B BE F3 109.47 5.0

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
08T sp3_sp3_1 PB O3A PA O2A 60.000 10.0 3
08T sp3_sp3_2 "C5'" "O5'" PA O2A 60.000 10.0 3
08T sp2_sp3_1 C4 N9 "C1'" "C2'" 150.000 20.0 6
08T const_0 N3 C2 N1 C6 0.000 0.0 1
08T const_1 N6 C6 N1 C2 180.000 0.0 1
08T const_2 N1 C2 N3 C4 0.000 0.0 1
08T const_3 N9 C4 N3 C2 180.000 0.0 1
08T sp3_sp3_3 PA O3A PB O1B 60.000 10.0 3
08T const_4 N3 C4 C5 C6 0.000 0.0 1
08T const_5 N3 C4 N9 "C1'" 0.000 0.0 1
08T const_6 C4 C5 C6 N6 180.000 0.0 1
08T const_7 C4 C5 N7 C8 0.000 0.0 1
08T sp2_sp2_1 N1 C6 N6 H12 0.000 5.0 2
08T const_8 N9 C8 N7 C5 0.000 0.0 1
08T const_9 N7 C8 N9 "C1'" 180.000 0.0 1
08T sp3_sp3_4 "C4'" "C5'" "O5'" PA 180.000 10.0 3
08T sp3_sp3_5 "C3'" "C4'" "C5'" "O5'" 180.000 10.0 3
08T sp3_sp3_6 "C5'" "C4'" "O4'" "C1'" 60.000 10.0 3
08T sp3_sp3_7 "O3'" "C3'" "C4'" "C5'" 60.000 10.0 3
08T sp3_sp3_8 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3
08T sp3_sp3_9 "C4'" "C3'" "O3'" H5 180.000 10.0 3
08T sp3_sp3_10 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3
08T sp3_sp3_11 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3
08T sp3_sp3_12 "C3'" "C2'" "O2'" H7 180.000 10.0 3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
08T chir_1 PA O3A "O5'" O1A both
08T chir_2 PB O3A O3B O2B both
08T chir_3 "C4'" "O4'" "C3'" "C5'" negative
08T chir_4 "C3'" "O3'" "C4'" "C2'" positive
08T chir_5 "C2'" "O2'" "C1'" "C3'" negative
08T chir_6 "C1'" "O4'" N9 "C2'" negative

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
08T plan-1 C2 0.020
08T plan-1 C4 0.020
08T plan-1 C5 0.020
08T plan-1 C6 0.020
08T plan-1 H10 0.020
08T plan-1 N1 0.020
08T plan-1 N3 0.020
08T plan-1 N6 0.020
08T plan-1 N7 0.020
08T plan-1 N9 0.020
08T plan-2 "C1'" 0.020
08T plan-2 C4 0.020
08T plan-2 C5 0.020
08T plan-2 C6 0.020
08T plan-2 C8 0.020
08T plan-2 H14 0.020
08T plan-2 N3 0.020
08T plan-2 N7 0.020
08T plan-2 N9 0.020
08T plan-3 C6 0.020
08T plan-3 H12 0.020
08T plan-3 H13 0.020
08T plan-3 N6 0.020

loop_
_chem_comp_ring_atom.comp_id
_chem_comp_ring_atom.ring_serial_number
_chem_comp_ring_atom.atom_id
_chem_comp_ring_atom.is_aromatic_ring
08T ring-1 C4' NO
08T ring-1 O4' NO
08T ring-1 C3' NO
08T ring-1 C2' NO
08T ring-1 C1' NO
08T ring-2 N1 YES
08T ring-2 C2 YES
08T ring-2 N3 YES
08T ring-2 C4 YES
08T ring-2 C5 YES
08T ring-2 C6 YES
08T ring-3 C4 YES
08T ring-3 C5 YES
08T ring-3 N7 YES
08T ring-3 C8 YES
08T ring-3 N9 YES

loop_
_acedrg_chem_comp_descriptor.comp_id
_acedrg_chem_comp_descriptor.program_name
_acedrg_chem_comp_descriptor.program_version
_acedrg_chem_comp_descriptor.type
08T acedrg 311 'dictionary generator'
08T 'acedrg_database' 12 'data source'
08T rdkit 2019.09.1 'Chemoinformatics tool'
08T servalcat 0.4.93 'optimization tool'
08T metalCoord 0.1.63 'metal coordination analysis'
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